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Chapter 9: Problem 15

Proline residues are almost never found in short \(\alpha\) -helices; nearly all transmembrane \(\alpha\) -helices that contain proline are long ones (about \(20 \text { residues }) .\) Suggest a reason for this observation.

Short Answer

Expert verified
Proline residues are less common in short alpha helices because proline's structure inhibits the formation of stabilizing hydrogen bonds, thus disrupting the helix. In long transmembrane alpha helices, however, the effect can be compensated by the rest of the structure. Furthermore, proline can induce a kink needed for transmembrane proteins to turn through the membrane's hydrophobic core.

Step by step solution

01

Structure of Proline

Proline is an amino acid. Unlike other amino acids, proline has a special structure where its side chain bonds to the amino group, creating a closed ring-like structure.
02

Proline in Alpha Helices

The alpha helix is a common protein structure stabilized by hydrogen bonds between the carbonyl group of a residue and the amino group of another residue four residues away. Because the side chain of proline is bonded to the amino group, it does not have the necessary hydrogen to participate in forming hydrogen bonds.
03

Effects on Alpha Helices

This lack of participation in hydrogen bonding makes proline a helix breaker, meaning it interrupts the regular formation of an alpha helix. This interruption would be particularly disruptive in short alpha helices, while in longer alpha helices, the disruption might be compensated by the rest of the structure.
04

Proline in Transmembrane Alpha Helices

In the case of long transmembrane alpha helices, it's suggested that the presence of proline introduces a necessary kink in the alpha helix for proteins to turn through the Hydrophobic (-CH2-) core of the membrane (a bend). This helps the protein conform to the membrane's geometry. Thus in this case, proline serves a crucial role despite its helix breaking properties.

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Most popular questions from this chapter

In the description of the mechanism of proton transport by bacteriorhodopsin, we find that light-driven conformation changes promote transmembrane proton transport. Suggest at least one reason for this behavior. In molecular terms, how could a conformation change facilitate proton transport?

(Integrates with Chapter 3 .) Fructose is present outside a cell at \(1 \mu M\) concentration. An active transport system in the plasma membrane transports fructose into this cell, using the free energy of ATP hydrolysis to drive fructose uptake. What is the highest intracellular concentration of fructose that this transport system can generate? Assume that one fructose is transported per ATP hydrolyzed; that ATP is hydrolyzed on the intracellular surface of the membrane; and that the concentrations of ATP, ADP, and \(P_{i}\) are \(3 \mathrm{m} M, 1 \mathrm{m} M,\) and \(0.5 \mathrm{m} M,\) respectively. \(T=298 \mathrm{K}\). (Hint: Refer to Chapter 3 to recall the effects of concentration on free energy of ATP hydrolysis.)

The purple patches of the Halobacterium halobium membrane, which contain the protein bacteriorhodopsin, are approximately \(75 \%\) protein and \(25 \%\) lipid. If the protein molecular weight is 26,000 and an average phospholipid has a molecular weight of 800 , calculate the phospholipid-to-protein mole ratio.

As described in the text, the \(\mathrm{pK}_{\mathrm{a}}\) values of Asp \(^{85}\) and \(\mathrm{Asp}^{96}\) of bacteriorhodopsin are shifted to high values (more than 11 ) because of the hydrophobic environment surrounding these residues. Why is this so? What would you expect the dissociation behavior of aspartate carboxyl groups to be in a hydrophobic environment?

In this chapter, we have examined coupled transport systems that rely on ATP hydrolysis, on primary gradients of \(\mathrm{Na}^{+}\) or \(\mathrm{H}^{+},\) and on phosphotransferase systems. Suppose you have just discovered an unusual strain of bacteria that transports rhamnose across its plasma membrane. Suggest experiments that would test whether it was linked to any of these other transport systems.
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